How to align two vertices on two planes?
While in the bigger User Ortho view, select the vertex you want to move, the one that cannot be moved in the Z axis. Once selected hit G, then Shift+Z (this allows the vertex to move in the X and Y axes, but not the Z axis). Then, holding Shift to limit movement speed and increase accuracy, visually line up the vertices. While not mathematically exact, you can zoom up quite close to ensure they are aligned to your liking.